Mitochondrial OXA Translocase Plays a Major Role in Biogenesis of Inner-Membrane Proteins

Abstract

The mitochondrial inner membrane harbors three protein translocases. Presequence translocase and carrier translocase are essential for importing nuclear-encoded proteins. The oxidase assembly (OXA) translocase is required for exporting mitochondrial-encoded proteins; however, different views exist about its relevance for nuclear-encoded proteins. We report that OXA plays a dual role in the biogenesis of nuclear-encoded mitochondrial proteins. First, a systematic analysis of OXA-deficient mitochondria led to an unexpected expansion of the spectrum of OXA substrates imported via the presequence pathway. Second, biogenesis of numerous metabolite carriers depends on OXA, although they are not imported by the presequence pathway. We show that OXA is crucial for the biogenesis of the Tim18-Sdh3 module of the carrier translocase. The export translocase OXA is thus required for the import of metabolite carriers by promoting assembly of the carrier translocase. We conclude that OXA is of central importance for the biogenesis of the mitochondrial inner membrane.

Graphical abstract

Figure 1

Mitochondrial Inner-Membrane Proteins Affected in OXA-Deficient Yeast Mutants (A) The levels of translocase core subunits and of Mdl1 of wild-type (WT) rho⁰, oxa1Δ, cox18Δ, and oxa1Δ cox18Δ mitochondria were analyzed by SDS-PAGE and immunoblotting. Mito., total mitochondrial protein; 100% represents 40 μg protein (80 μg for Sam50). (B) Differential analysis of the proteome of WT rho⁰ compared to oxa1Δ cox18Δ mitochondria using MS. WT rho⁰ and oxa1Δ cox18Δ cells were differentially labeled with stable isotopes, mixed and mitochondria were isolated and analyzed by quantitative MS (Table S1). Integral inner-membrane proteins found to be depleted in oxa1Δ cox18Δ mitochondria (heavy/light ratio >1.6) are listed with the yeast open reading frame (ORF). See also Figure S1, and Table S1, and Table S2.

Figure 2

Oxa1-Dependent Assembly of SDH Complex and TIM22 Complex (A) Protein levels of TIM22 and SDH subunits were analyzed in the indicated mitochondria by SDS-PAGE and immunoblotting. Mito., total mitochondrial protein; 100% represents 160 μg protein (40 μg for Sdh3 and Sdh4; 80 μg for Tim9 and Tim12). (B) SDH complex and TIM22 complex were analyzed by blue native electrophoresis of isolated mitochondria and immunoblotting. (C) Mitochondria were either heat shocked for 12 min at 37°C or incubated at 25°C, followed by import of [³⁵S]Tim18 precursor at 25°C. After Proteinase K treatment, assembly into the TIM22 complex was monitored by blue native electrophoresis and autoradiography. (D) After an in vitro heat shock of mitochondria, [³⁵S]Sdh4 precursor was imported at 30°C, followed by Proteinase K treatment. Assembly of SDH and the Sdh3-Sdh4 intermediate were analyzed by blue native electrophoresis. (E) Mitochondria were subjected to a heat shock, followed by import of [³⁵S]Aac2 and [³⁵S]Dic1 at 25°C and Proteinase K treatment. Carrier assembly was monitored by blue native electrophoresis. (F) Protein levels were analyzed by SDS-PAGE and immunoblotting. Mito., total mitochondrial protein; 100% represents 40 μg protein. (G) Dic1 was imported into mitochondria. After Proteinase K treatment, carrier assembly was monitored by blue native electrophoresis. See also Figures S2 and S3 and Table S2.

Figure 3

Mitochondrial Sorting of Sdh4 and Tim18 Depends on the mtHsp70 Import Motor (A–C) Import of ³⁵S-labeled Sdh4 (A), Tim18 (B), Aac2 and Dic1 (C) into in vitro heat-shocked (37°C for 12–15 min) wild-type (WT), ssc1-3, and pam16-3 mitochondria at 25°C (30°C for A, lanes 1–8), followed by Proteinase K treatment. Arrowhead, unspecific band. (D–G) ³⁵S-labeled Sdh4 (D and E) or TM3 fused to the Sdh4 presequence, [³⁵S]Sdh4_TM3 (F and G), were imported into WT, oxa1-ts, and ssc1-3 mutant mitochondria at 30°C. WT and mutant mitochondria were heat shocked prior to the import reaction. Nonimported [³⁵S]Sdh4_TM3 was removed by Proteinase K treatment. After washing, mitochondria were suspended in either isotonic buffer (−swelling) or hypotonic buffer (+swelling). Where indicated, Proteinase K or trypsin was added. The mitochondrial samples were analyzed by SDS-PAGE and autoradiography. p, precursor; m, mature form; Sdh4′ and Sdh4_TM3′, protease-protected Sdh4 and Sdh4_TM3 fragments. Cartoons in (D) and (F): the TMs of Sdh4 are numbered from 1 to 3; IM, inner membrane; IMS, intermembrane space. See also Figure S4 and Table S2.

Figure 4

Role of OXA in the Biogenesis of Nuclear-Encoded Inner-Membrane Proteins (A and B) Mitochondria isolated from the indicated yeast cells were either subjected to SDS-PAGE or lysed with 1% digitonin and analyzed by blue native electrophoresis, followed by immunoblotting. Mito., total mitochondrial protein; 100% represents 160 μg protein (40 μg for Tim13 and Yme1; 80 μg for Atm1 and Mdl1; 320 μg for Ndi1). (C) Samples 1–4, the indicated mitochondria were lysed with digitonin and analyzed by blue native electrophoresis and immunoblotting. Samples 5–28, mitochondria were subjected to a heat shock where indicated; Mmt1 and Mmt2 were imported, followed by Proteinase K treatment. Mitochondria were analyzed by blue native electrophoresis and autoradiography. (D) Heat-treated (15 min 37°C) mitochondria were incubated with Mmt2 or Coq2 precursors at 25°C, followed by Proteinase K treatment and SDS-PAGE. (E) Model of Oxa1 function in the biogenesis of nuclear-encoded mitochondrial inner-membrane proteins. Cyto., cytosol; OM, outer membrane; IMS, intermembrane space; IM, inner membrane. See also Figure S4.